Relative Isolation Research Articles

Evaluating Fourier-transform infrared spectroscopy with IR Biotyper as a faster and simpler method for investigating the sources of an outbreak of legionellosis.

Fourier-transform infrared (FTIR) spectroscopy using the IR Biotyper and core genome singlenucleotide polymorphism (cgSNP) analysis were performed on 12 Legionella isolates associated with an outbreak at a spa house in Kanagawa Prefecture, Japan, and 3 non-outbreak isolates. The discriminative power of FTIR spectroscopy for 48-h incubation conditions of L. pneumophila in this outbreak was lower than cgSNP-based typing but higher than serogroup typing. FTIR spectroscopy could screen outbreak isolates from a group of genetically related isolates and may be useful as an initial typing method in Legionella outbreak investigations.

Tales from the end of the world: three decades of paleogenetic research in Patagonia

Patagonia is a region that has fascinated researchers for centuries considering the evidence of early human occupation, its geographical and environmental variability, and the diversity of human adaptations. From an archaeological and bioanthropological perspective, the region has been the focus of many studies addressing a wide range of questions, from a broad scale, such as the peopling of the Americas, to a local scale concerning the diversity and interactions of human populations. For three decades, paleogenetic studies have contributed to the understanding of population dynamics in the region: first using uniparental markers, particularly mitochondrial DNA in a much larger proportion; and more recently including genome-wide data for ancient individuals. In this work, we revise these studies considering three themes: (1) the first stages of migration into the region; (2) the diversification and interactions of populations during the Middle and Late Holocene; and (3) the link between present-day and ancient populations. While genetic evidence from the early peopling stages is either absent or scarce, making it difficult to evaluate the relative contributions of early South American lineages in the first Patagonian populations, evidence from later periods (from Middle Holocene onwards) is consistent with a single migration wave with founding events and genetic drift acting on small groups during their migration southward. After the initial occupation, the population dynamics seem to have been characterised by the relative isolation of different groups, leading to their differentiation. While there is evidence of some degree of gene flow between groups, the genetic structure in the region is generally associated with geography, subsistence systems, and languages. After European contact, paleogenetic data supports a relative genetic continuity in the region. We finish this review with a fourth theme in which we reflect on the current state and direction of the field in Patagonia, highlighting research lines that will benefit from the implementation of state-of-the-art paleogenomic approach, as well as legal and ethical considerations that would allow to move forward into a more collaborative and inclusive field.

Phenotypic and genetic characterization of antimicrobial resistance in Salmonella enterica serovar Choleraesuis isolates from humans and animals in Spain from 2006 to 2021.

While an increase in the levels of MDR in Salmonella enterica sevorar Choleraesuis has been reported in Europe, little is known about the situation in Spain. Therefore, we first aimed to assess the phenotypic resistance profile and to determine the presence of genetic determinants of resistance of S. Choleraesuis isolates collected in animal and human. Our second objective was to identify and characterize clusters of highly related isolates. We analysed 50 human and 45 animal isolates retrieved from 2006 to 2021 using the disc diffusion method and performed WGS followed by analyses of genetic determinants and phylogenetic analysis. All isolates were of ST145 and corresponded to the variant Kunzendorf. Swine isolates harboured a significantly higher number of antimicrobial resistance genes than human isolates, and often carried plasmid replicons of the IncHI2/IncHI2A type (42% of all animal isolates). In addition, we identified several MDR S. Choleraesuis strains circulating in humans and swine between 2006 and 2021. The phylogenetic analyses identified four clades associated with specific patterns of resistance genes and plasmid replicons. The clades also included isolates that differed in terms of year and region of isolation as well as host of origin. This One Health approach highlights that reducing human MDR S. Choleraesuis infections may require the adoption of strategies that not only seek to prevent cases in humans but also to characterize and reduce the infection burden in swine.

Rare serotype c Haemophilus influenzae invasive isolate: characterization of the first case in Portugal.

We report for the first time in Portugal a serotype c Haemophilus influenzae isolated from an adult, with HIV-1 infection. Whole-genome sequencing characterized the isolate as clonal complex ST-7, albeit with a novel MLST (ST2754) due to a unique atpG profile. Integration of this genome with other available H. influenzae serotype c genomes from PubMLST revealed its overall genetic distinctiveness, with the closest related isolate being identified in France in 2020. This surveillance study, involving collaboration among hospitals and reference laboratory, successfully contributed to the identification and characterization of this rare serotype.

Where Asylum and Austerity Meet: Deservingness and In/Exclusion in Rochdale

AbstractThe UK's asylum and social welfare systems have both been transformed by major organisational changes, funding cuts, and privatisations through a decade of austerity. With this, asylum‐seeker accommodation and the impacts of welfare reform have become increasingly concentrated in already‐impoverished, peripheral urban areas such as Rochdale, Greater Manchester. Despite these parallels, scholarship and commentary in the UK has tended to consider welfare and border regimes in relative isolation. Based on ethnographic work conducted in two charity drop‐centres in the town, this article addresses this gap by exploring how the UK's converging politics and geographies of asylum and welfare governance shape everyday negotiations of deservingness and social in/exclusion.

Rapid typing of Klebsiella pneumoniae and Pseudomonas aeruginosa by Fourier-transform Infrared spectroscopy informs infection control in veterinary settings.

The emergence of multi-drug resistant (MDR) pathogens linked to healthcare-associated infections (HCAIs) is an increasing concern in modern veterinary practice. Thus, rapid bacterial typing for real-time tracking of MDR hospital dissemination is still much needed to inform best infection control practices in a clinically relevant timeframe. To this end, the IR Biotyper using Fourier-Transform InfraRed (FTIR) spectroscopy has the potential to provide fast cluster analysis of potentially related organisms with substantial cost and turnaround time benefits. A collection of MDR bacterial isolates (n = 199, comprising 92 Klebsiella pneumoniae and 107 Pseudomonas aeruginosa) obtained from companion animal (i.e., dogs, cats and horses) clinical investigations, faecal and environmental screening from four veterinary facilities between 2012 and 2019 was analysed retrospectively by FTIR spectroscopy. Its performance was compared against MLST extracted from whole genomes of a subset of clustering isolates (proportionally to cluster size) for investigation of potential nosocomial transmission between patients and the surrounding hospital environments. Concordance between the FTIR and MLST types was overall high for K. pneumoniae (Adjusted Rand Index [ARI] of 0.958) and poor for P. aeruginosa (ARI of 0.313). FTIR K. pneumoniae clusters (n = 7) accurately segregated into their respective veterinary facility with evidence of intra-hospital spread of K. pneumoniae between patients and environmental surfaces. Notably, K. pneumoniae ST147 intensely circulated at one Small Animal Hospital ICU. Conversely, Pseudomonas aeruginosa FTIR clusters (n = 18) commonly contained isolates of diversified hospital source and heterogeneous genetic background (as also genetically related isolates spread across different clusters); nonetheless, dissemination of some clones, such as P. aeruginosa ST2644 in the equine hospital, was apparent. Importantly, FTIR clustering of clinical, colonisation and/or environmental isolates sharing genomically similar backgrounds was seen for both MDR organisms, highlighting likely cross-contamination events that led to clonal dissemination within settings. FTIR spectroscopy has high discriminatory power for hospital epidemiological surveillance of veterinary K. pneumoniae and could provide sufficient information to support early detection of clonal dissemination, facilitating implementation of appropriate infection control measures. Further work and careful optimisation need to be carried out to improve its performance for typing of P. aeruginosa veterinary isolates.

Environmental fate of microplastics in alpine and canyon-type river-cascade reservoir systems: Large-scale investigation of the Yalong River in the eastern Qinghai-Tibet Plateau

Reservoirs are regarded as potential collection sites for microplastics (MPs), and ample water resources in plateau regions provide favorable natural conditions for hydroelectric power generation. However, research on the impact of cascade reservoir construction in the plateau region on the fate of MPs within the watershed is limited. In this study, the Yalong River, an alpine canyon river in the eastern Qinghai-Tibet Plateau, was selected as the research area. This study explored the distribution of MPs at various depths in water, sediment, and riverbank soil as well as the formation of “MP communities” within the river-cascade reservoir system. Furthermore, the effects of dam construction on MPs' migration in different environments were analyzed. The results revealed that the abundance of MPs in the water and sediment within the cascade reservoir area (CRA) was significantly higher than that in the river area (RA) (P < 0.001). Additionally, the trend of increasing MPs in water with decreasing altitude was notably slower in CRA. Regarding shape, the proportion of fibers in the water within the CRA was significantly lower than that in the RA, with a smaller vertical migration rate in the water than in the sediment. The proportion of MPs < 500 μm in the water within the CRA was significantly higher than that in the RA. High-density MPs were notably deposited in the reservoir sediments. The analysis of the MP communities revealed that the construction of cascade dams led to relative geographical isolation between different sampling sites, reducing the similarity of MP communities in the CRA. This study established a theoretical foundation for understanding the impact of cascade dam construction on the fate characteristics of MPs and their potential risks in plateau areas.

Genomic description of acquired fluconazole- and echinocandin-resistance in patients with serial Candida glabrata isolates.

Candida glabrata is one of the most common causes of systemic candidiasis, often resistant to antifungal medications. To describe the genomic context of emerging resistance, we conducted a retrospective analysis of 82 serially collected isolates from 33 patients from population-based candidemia surveillance in the United States. We used whole-genome sequencing to determine the genetic relationships between isolates obtained from the same patient. Phylogenetic analysis demonstrated that isolates from 29 patients were clustered by patient. The median SNPs between isolates from the same patient was 30 (range: 7-96 SNPs), while unrelated strains infected four patients. Twenty-one isolates were resistant to echinocandins, and 24 were resistant to fluconazole. All echinocandin-resistant isolates carried a mutation either in the FKS1 or FKS2 HS1 region. Of the 24 fluconazole-resistant isolates, 17 (71%) had non-synonymous polymorphisms in the PDR1 gene, which were absent in susceptible isolates. In 11 patients, a genetically related resistant isolate was collected after recovering susceptible isolates, indicating in vivo acquisition of resistance. These findings allowed us to estimate the intra-host diversity of C. glabrata and propose an upper boundary of 96 SNPs for defining genetically related isolates, which can be used to assess donor-to-host transmission, nosocomial transmission, or acquired resistance. IMPORTANCE In our study, mutations associated to azole resistance and echinocandin resistance were detected in Candida glabrata isolates using a whole-genome sequence. C. glabrata is the second most common cause of candidemia in the United States, which rapidly acquires resistance to antifungals, in vitro and in vivo.

Covid-19 related isolation and risk of post-traumatic stress disorder in patients presenting to tele-clinics at a private tertiary care hospital in Karachi.

The objective of this study was to assess the psychological impact of isolation on individuals with Covid-19 and determine the experiences of people in isolation. All adults with Covid-19 who reported to the infectious disease tele-clinic were included in the study; participants were sent the survey form via email. The email was sent to 146 people and 47 responses were received. IES-R questionnaire was submitted to all individuals on Day 7 of quarantine, along with a qualitative questionnaire. The mean score on IES-R for all the respondents was 18.77. Out of 47 participants, for 6 (12.8%) PTSD was a clinical concern, 3 (6.4%) participants had a probable diagnosis of PTSD, and 6 (12.8%) participants scored high enough to suppress immune function. The majority of participants reported stress due to confinement in an isolated space and interruption in daily routine, specifically work-related routine. Praying, meditation, and having social support helped the participants cope with the isolation.

Moderators of Loneliness Trajectories in People with Systemic Sclerosis During the COVID-19 Pandemic: A SPIN COVID-19 Cohort Longitudinal Study.

Many individuals with systemic sclerosis (SSc) are at heightened risk for COVID-19 related morbidity and isolation due to interstitial lung disease, frailty, and immunosuppressant use. Minimal research has explored loneliness predictors in individuals with chronic illnesses during COVID-19. This study evaluated moderators of loneliness trajectories in individuals with SSc during COVID-19. Longitudinal data were analyzed across 30 timepoints from April 2020 to May 2022 from 775 adults in the Scleroderma Patient-centered Intervention Network (SPIN) COVID-19 Cohort. Hierarchical linear modeling evaluated cross-level moderators of loneliness trajectories, including marital status, baseline number of household members, number of virtual or telephone one-on-one or virtual group conversations, number of hours spent enjoying in-person household conversations or activities, and satisfaction with quality of in-person household conversations (all in the past week). Level-1 moderation analyses assessed effects of conversation, activity, and satisfaction means and slopes over time. Baseline values were not statistically significant moderators of loneliness trajectories. Higher mean (averaged over time) virtual or telephone one-on-one and in-person household conversations, in-person household activity, and in-person household conversation satisfaction were associated with lower loneliness trajectories (ps < .05). The relationship between in-person household conversation satisfaction and loneliness trajectory was statistically significantly but minimally attenuated over time (p < .001). For people with SSc, higher mean conversation, activity, and satisfaction variables were associated with lower levels of loneliness during the pandemic, but changes in these social variables were generally not predictive of changes in loneliness.

Multilocus sequence typing schemes for the emerging swine pathogen Mycoplasma hyosynoviae

Mycoplasma (M.) hyosynoviae is a commensal of the upper respiratory tract in swine, which has the potential to spread systemically, usually resulting in arthritis in fattening pigs and gilts. To date, very little is known about the epidemiology of M. hyosynoviae, mainly due to a lack of suitable typing methods. Therefore, this study aimed to develop both a conventional multi locus sequence typing (MLST) and a core genome (cg) MLST scheme. The development of the cgMLST was based on whole genome sequences of 64 strains isolated from pigs and wild boars during routine diagnostics as well as nine publicly available genomes. A cgMLST scheme containing 390 target genes was established using the Ridom© SeqSphere+ software. Using this scheme as a foundation, seven housekeeping genes were selected for conventional MLST based on their capability to reflect genome wide relatedness and subsequently, all 73 strains were typed by applying both methods. Core genome MLST results revealed a high diversity of the studied strain population and less than 100 allele differences between epidemiologically unrelated strains were only detected for four isolates from the US. On the other hand, seven clonal clusters (≤ 12 allele differences) comprising 20 isolates were identified. Comparison of the two typing methods resulted in highly congruent phylogenetic trees and an Adjusted Rand Coefficient of 0.893, while cgMLST showed marginally higher resolution when comparing closely related isolates, indicated by a slightly higher Simpson’s ID (0.992) than conventional MLST (Simpson’s ID = 0.990). Overall, both methods seem well suited for epidemiological analyses for scientific as well as diagnostic purposes. While MLST is faster and cheaper, cgMLST can be used to further differentiate closely related isolates.

Recovery and genetic characterization of clinically-relevant ST2 carbapenem-resistant Acinetobacter baumannii isolates from untreated hospital sewage in Zhejiang Province, China

The global transmission of carbapenem-resistant Acinetobacter baumannii (CRAB) poses a significant and grave threat to human health. To investigate the potential relationship between hospital sewage and the transmission of CRAB within healthcare facilities, isolates of Acinetobacter spp. obtained from untreated hospital sewage samples were subjected to antimicrobial susceptibility tests, genome sequencing, and bioinformatic and phylogenetic tree analysis, and that data were matched with those of the clinical isolates. Among the 70 Acinetobacter spp. sewage isolates tested, A. baumannii was the most prevalent and detectable in 5 hospitals, followed by A. nosocomialis and A. gerneri. Worryingly, 57.14 % (40/70) of the isolates were MDR, with 25.71 % (18/70) being resistant to carbapenem. When utilizing the Pasteur scheme, ST2 was the predominant type among these CRAB isolates, with Tn2006 (ΔISAba1-blaOXA-23-ATPase-yeeB-yeeA-ΔISAba1) and Tn2009 (ΔISAba1-blaOXA-23-ATPase-hp-parA-yeeC-hp-yeeB-ΔISAba1) being the key mobile genetic elements that encode carbapenem resistance. Seven A. gerneri isolates which harbored Tn2008 (ISAba1-blaOXA-23 -ATPase) and the blaPER-1 gene were also identified. Besides, an A. soil isolate was found to exhibit high-level of meropenem resistance (MIC ≥128 mg/L) and harbor a blaNDM-1 gene located in a core genetic structure of ISAba125-blaNDM-1-ble-trpF-dsbC-cutA. To investigate the genetic relatedness between isolates recovered from hospital sewage and those collected from ICUs, a phylogenetic tree was constructed for 242 clinical isolates and 9 sewage isolates. The results revealed the presence of two evolutionary clades, each containing isolates from both ICU and sewage water, suggesting that CRAB isolates in untreated sewage water were also the transmission clones or closely related evolutionary isolates recoverable in hospital settings. Findings in this work confirm that hospital sewage is a potential reservoir of CRAB.

Genomic characterization of Pseudomonas spp. on food: implications for spoilage, antimicrobial resistance and human infection

BackgroundPseudomonas species are common on food, but their contribution to the antimicrobial resistance gene (ARG) burden within food or as a source of clinical infection is unknown. Pseudomonas aeruginosa is an opportunistic pathogen responsible for a wide range of infections and is often hard to treat due to intrinsic and acquired ARGs commonly carried by this species. This study aimed to understand the potential role of Pseudomonas on food as a reservoir of ARGs and to assess the presence of potentially clinically significant Pseudomonas aeruginosa strains on food. To achieve this, we assessed the genetic relatedness (using whole genome sequencing) and virulence of food-derived isolates to those collected from humans.ResultsA non-specific culturing approach for Pseudomonas recovered the bacterial genus from 28 of 32 (87.5%) retail food samples, although no P. aeruginosa was identified. The Pseudomonas species recovered were not clinically relevant, contained no ARGs and are likely associated with food spoilage. A specific culture method for P. aeruginosa resulted in the recovery of P. aeruginosa from 14 of 128 (11%) retail food samples; isolates contained between four and seven ARGs each and belonged to 16 sequence types (STs), four of which have been isolated from human infections. Food P. aeruginosa isolates from these STs demonstrated high similarity to human-derived isolates, differing by 41–312 single nucleotide polymorphisms (SNPs). There were diverse P. aeruginosa collected from the same food sample with distinct STs present on some samples and isolates belonging to the same ST differing by 19–67 SNPs. The Galleria mellonella infection model showed that 15 of 16 STs isolated from food displayed virulence between a low-virulence (PAO1) and a high virulence (PA14) control.ConclusionThe most frequent Pseudomonas recovered from food examined in this study carried no ARGs and are more likely to play a role in food spoilage rather than infection. P. aeruginosa isolates likely to be able to cause human infections and with multidrug resistant genotypes are present on a relatively small but still substantial proportions of retail foods examined. Given the frequency of exposure, the potential contribution of food to the burden of P. aeruginosa infections in humans should be evaluated more closely.

Novel and reported compensatory mutations in rpoABC genes found in drug resistant tuberculosis outbreaks.

Rifampicin (RIF) is a key first-line drug used to treat tuberculosis, a primarily pulmonary disease caused by Mycobacterium tuberculosis. RIF resistance is caused by mutations in rpoB, at the cost of slower growth and reduced transcription efficiency. Antibiotic resistance to RIF is prevalent despite this fitness cost. Compensatory mutations in rpoABC genes have been shown to alleviate the fitness cost of rpoB:S450L, explaining how RIF resistant strains harbor this mutation can spread so rapidly. Unfortunately, the full set of RIF compensatory mutations is still unknown, particularly those compensating for rarer RIF resistance mutations. We performed an association study on a globally representative set of 4,309 whole genome sequenced clinical M. tuberculosis isolates to identify novel putative compensatory mutations, determine the prevalence of known and previously reported putative compensatory mutations, and determine which RIF resistance markers associate with these compensatory mutations. Of the 1,079 RIF resistant isolates, 638 carried previously reported putative and high-probability compensatory mutations. Our strict criteria identified 46 additional mutations in rpoABC for which no strong prior evidence of their compensatory role exists. Of these, 35 have previously been reported. As such, our independent corroboration adds to the mounting evidence that these 35 also carry a compensatory role. The remaining 11 are novel putative compensatory markers, reported here for the first time. Six of these 11 novel putative compensatory mutations had two or more mutation events. Most compensatory mutations appear to be specifically compensating for the fitness loss due to rpoB:S450L. However, an outbreak of 22 closely related isolates each carried three rpoB mutations, the rare RIFR markers D435G and L452P and the putative compensatory mutation I1106T. This suggests compensation may require specific combinations of rpoABC mutations. Here, we report only mutations that met our very strict criteria. It is highly likely that many additional rpoABC mutations compensate for rare resistance-causing mutations and therefore did not carry the statistical power to be reported here. These findings aid in the identification of RIF resistant M. tuberculosis strains with restored fitness, which pose a greater risk of causing resistant outbreaks.

The intrinsic and extrinsic drivers of extinction risk in lemurs (Lemuroidea)

Understanding why some species are more susceptible to extinction than others is critical for implementing effective conservation strategies. Phylogenetic comparative methods (PCMs) have been used to understand the drivers of extinction risk, and are most effective when applied to an entire lineage. Lemurs are a monophyletic group that evolved in Madagascar in relative isolation over millions of years, representing a unique and diverse lineage that provides an excellent case study for the drivers of extinction risk. We investigated the drivers of extinction risk in lemurs using intrinsic (species' traits) and extrinsic (environmental) variables related to ecology, life-history, and biogeography. We evaluated the tempo and mode of trait evolution and used PCMs to examine correlations between traits and extinction risk. We used models of trait evolution and historic and future climate data to predict how lemurs will fare under climate change. The predominant drivers of extinction risk in lemurs were diurnal activity and longevity, which were positively and negatively associated with extinction risk, respectively. Body size, as well as temperature mean and temperature variance across a species' range, were also predictors of risk. We found no evidence for evolution punctuated by short periods of rapid change in response to environmental shifts or other factors (punctuated equilibria), suggesting that traits will not evolve to track Madagascar's changing climate. These results may inform conservation strategies in Madagascar by differentiating the role of intrinsic vs. extrinsic traits in extinction risk. Moreover, findings may contribute to preventing declines in other endangered and endemic taxonomic groups.

Catechol-type siderophore producer Streptomyces spp. with quorum-quenching activity isolated from wild medicinal plants rhizosphere

Traditional medicinal plants represent a unique source for the isolation of Streptomycetes and antimicrobial compounds. Antimicrobial activity of Streptomyces isolates collected from the rhizosphere of different native medicinal plants in Iran, was investigated against Gram-positive and Gram-negative bacteria. Multi-omics analysis was performed to identify active compounds corresponding to the observed bioactivities. Since cell-to-cell communication mediated by N-acyl homoserine lactones (AHLs) is important for the virulence of Gram-negative pathogenic bacteria, quorum quenching activity of the isolates and their ability to degrade C6-HSL and C8-HSL were tested. Two highly related Streptomyces isolates derived from the Helichrysum rubicundum and Rumex acetosa rhizosphere, respectively, exhibited bioactivity against pathogenic indicator bacteria. Metabolite analysis of extracts obtained from liquid cultures of both isolates revealed the production of the catechol-peptide siderophores streptobactin and tribenarthin. Proteomic analysis confirmed the presence of proteins encoded by the streptobactin and lidamycin biosynthetic gene clusters. Quorum quenching activity of the strains and AHL-degrading enzyme production was confirmed using a GFP producing biosensor and LC-MS analysis. This study demonstrates catecholate siderophore production and QQ potential of two Streptomyces isolates from medicinal plants rhizosphere from Mishan Plain, Hamedan Province, Iran using metabolomics and proteomics analysis. Production of streptobactin by terrestrial Streptomyces sp. strains was confirmed for the first time.

Phylogenetic Characterization of Resistant Salmonella Strains in Typhoid Fever Patients in Nigeria.

Salmonella species are Enterobacteriaceae associated with typhoid fever. In this study, the distribution of broad-spectrum β-lactamase regulatory genes and genetic relatedness of isolates was determined. Stool samples (400) were collected from patients with fever in Dalhatu Araf Specialist Hospital (DASH), Lafia, Nigeria, between March 2020 and April 2021. Salmonella species were isolated and extended-spectrum β-lactamase distribution was determined among resistant isolates using polymerase chain reaction (PCR). Genetic relatedness of Salmonella species resistant to the 10 first-line antibiotics administered was determined among S typhi isolated. Of the 60 isolates that were confirmed to belong to the genus Salmonella, 12 (20.0%) isolates with bla SHV genes were the most prevalent, blaOXA-1 and blaCTX-M-9 were present in 5 isolates each, while blaCTX-M-4 and blaTEM genes with a prevalence of 1.7% each were the least obtained in the isolates. Two isolates had a multidrug-resistant index (MDRI) of 1, and 2 others were positive with the S typhi staG gene. Sequencing to determine their diversity showed that isolates ST36 and ST138, respectively, had MDRI = 1 and are clustered in a group with a similarity coefficient of 0.00634. The 2 isolates had the highest genetic similarity, which indicates that the genetic diversity between the isolates is low, while Salmonella strain ST313L2 had a high level of genetic distance from the other isolates. The most resistant isolates are closely related which calls for concern.

An empirical study of interdisciplinary crime research

Abstract This research was designed to test the effectiveness of interdisciplinary scientific research in the field of crime. A survey was conducted using an online questionnaire to assess the hypotheses and evaluate the adequacy of statistical and text analysis tools. The sample consisted of scientists from various disciplines. The results of the data analysis showed that there is a lack of effective interdisciplinary cooperation and knowledge synthesis among the different types of sciences. Interdisciplinarity in science involves the synthesis and application of knowledge from different scientific fields. In the field of crime research, there is a lack of organized interdisciplinary approaches due to the relative isolation of various scientific disciplines and their focus on traditional research subjects. This means that crime is often not a priority for these disciplines. The discussion chapter examined the factors contributing to the less effective interdisciplinary research in the field of crime, as well as explored the potential for achieving a more effective synthesis of knowledge in criminology.

Clonal spread of trimethoprim-sulfamethoxazole-resistant Stenotrophomonas maltophilia isolates in a tertiary hospital.

The aims of this study were to: (i) determine antibiotic susceptibility of clinical Stenotrophomonas maltophilia isolates, (ii) investigate the presence of different classes of integrons and sul genes responsible for sulphonamide resistance, (iii) assess the molecular epidemiology of the isolates by determining their clonal relatedness, and (iv) investigate the potential sources of infection by collecting environmental samples when necessary. 99 S. maltophilia isolates from clinical specimens of hospitalized patients were screened by PCR for sul1, sul2, sul3 genes, and integron-associated integrase genes: intI1, intI2, and intI3. PFGE was used to determine the clonal relatedness of the isolates. Susceptibility rates for trimethoprim-sulfamethoxazole, levofloxacin, and ceftazidime were 90.9%, 91.9%, and 53.5% respectively. All trimethoprim-sulfamethoxazole-resistant isolates were positive for intI1 and sul1. PFGE analysis revealed that 24 of the isolates were clonally related, clustering in seven different clones. Five of the nine trimethoprim-sulfamethoxazole-resistant isolates were clonally related. The first isolate in this clone was from a wound sample of a patient in the infectious diseases clinic, and the other four were isolated from the bronchoalveolar lavage samples of patients in the thoracic surgery unit. The patient with the first isolate neither underwent bronchoscopy nor stayed in the thoracic surgery unit. Although clustering was observed in bronchoalveolar lavage samples, no S. maltophilia growth was detected in environmental samples. The findings demonstrated that the sul1 gene carried by class 1 integrons plays an important role in trimethoprim-sulfamethoxazole resistance in S. maltophilia isolates. PFGE analysis revealed a high degree of genetic diversity. However, detection of clonally related isolates suggests the acquisition from a common source and/or cross-transmission of this microorganism between the patients.

First Canadian report of transmission of fluconazole-resistant Candida parapsilosis within two hospital networks confirmed by genomic analysis.

Candida parapsilosis is a common cause of non-albicans candidemia. It can be transmitted in healthcare settings resulting in serious healthcare-associated infections and can develop drug resistance to commonly used antifungal agents. Following a significant increase in the percentage of fluconazole (FLU)-nonsusceptible isolates from sterile site specimens of patients in two Ontario acute care hospital networks, we used whole genome sequence (WGS) analysis to retrospectively investigate the genetic relatedness of isolates and to assess potential in-hospital spread. Phylogenomic analysis was conducted on all 19 FLU-resistant and seven susceptible-dose dependent (SDD) isolates from the two hospital networks, as well as 13 FLU susceptible C. parapsilosis isolates from the same facilities and 20 isolates from patients not related to the investigation. Twenty-five of 26 FLU-nonsusceptible isolates (resistant or SDD) and two susceptible isolates from the two hospital networks formed a phylogenomic cluster that was highly similar genetically and distinct from other isolates. The results suggest the presence of a persistent strain of FLU-nonsusceptible C. parapsilosis causing infections over a 5.5-year period. Results from WGS were largely comparable to microsatellite typing. Twenty-seven of 28 cluster isolates had a K143R substitution in lanosterol 14-α-demethylase (ERG11) associated with azole resistance. As the first report of a healthcare-associated outbreak of FLU-nonsusceptible C. parapsilosis in Canada, this study underscores the importance of monitoring local antimicrobial resistance trends and demonstrates the value of WGS analysis to detect and characterize clusters and outbreaks. Timely access to genomic epidemiological information can inform targeted infection control measures.